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API Phonons is a Python software package to predict the transport dynamics of heat-carrying phonons. Using the powerful syntax of Python, this package provides modules and functions interfacing between different packages for atomistic simulations, lattice dynamics, and phonon-phonon interaction calculations including LAMMPS, Quippy, Phonopy, and ShengBTE. API Phonons enabled complex phonon calculations, including (1) extracting harmonic and anharmonic force constants from arbitrary interatomic potentials, which can be used as inputs for solving Boltzmann transport equations; (2) predicting thermal conductivity using Kubo's linear response theory, which captures both quasiparticle transport and inter-band coherent transport; and (3) modeling of ultrafast pump-probe thermal responses using a Green's function approach based on mode-resolved phonon properties for studying ballistic, hydrodynamic, and diffusive transport dynamics. The package provides a flexible, easy-to-use, and extensive platform for modeling phonon transport physics through Python programming.